Opal Web Services for Biomedical Applications

Opal Web Services for Biomedical Applications provides scalable, standards-based programmatic access to biomedical scientific applications as web services to enable deployment and execution of bioinformatics tools such as MEME, AutoDock, AutoDock Vina, PDB2PQR, APBS, and SMAP on high-performance computing resources.

Key Features:

• Scientific Software as a Service (sSaaS): Exposes biomedical applications as remotely executable services enabling execution on computational resources.
• Comprehensive Application Support: Hosts bioinformatics applications including MEME, AutoDock, AutoDock Vina, PDB2PQR, APBS, and SMAP for motif discovery, docking, electrostatic calculations, and off-target analysis.
• Opal Toolkit Integration: Wraps scientific applications as web services using XML configuration files without requiring modification of the original codebase.
• SOAP-Based Web Service Access: Supports SOAP-based web service protocols for interoperable programmatic access.
• Workflow Tool Compatibility: Enables programmatic integration with workflow systems such as Vision, Kepler, Nimrod/K, and VisTrails.
• Scalability and Usage: Demonstrated production-scale execution with over 239,814 jobs run and daily job executions increasing from 205 to 411 between 2008 and 2009.

Scientific Applications:

• Sequence motif discovery (MEME): Runs MEME for identifying conserved sequence motifs from biological sequence data.
• Molecular docking (AutoDock, AutoDock Vina): Executes AutoDock and AutoDock Vina for protein–ligand docking and binding pose prediction.
• Electrostatic calculations (PDB2PQR, APBS): Performs structure preparation with PDB2PQR and continuum electrostatics calculations with APBS.
• Off-target structural analysis (SMAP): Runs SMAP for structure-based off-target identification and comparison.

Methodology:

The Opal toolkit wraps applications as SOAP-accessible web services via XML configuration files, enabling programmatic access and deployment to high-performance computing resources without modifying application code.